readHTSeqFile {GenomicDataCommons} | R Documentation |
The htseq package is used extensively to count reads relative to regions (see http://www-huber.embl.de/HTSeq/doc/counting.html). The output of htseq-count is a simple two-column table that includes features in column 1 and counts in column 2. This function simply reads in the data from one such file and assigns column names.
readHTSeqFile(fname, samplename = "sample", ...)
fname |
character(1), the path of the htseq-count file. |
samplename |
character(1), the name of the sample. This will
become the name of the second column on the resulting
|
... |
passed to |
a two-column data frame
fname = system.file(package='GenomicDataCommons', 'extdata/example.htseq.counts.gz') dat = readHTSeqFile(fname) head(dat)